swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties. For each match an empirical measure of statistical significance derived from the observed score distribution is computed.

Swat is licensed software and thus is not installed by default on Bio-Linux. It is free to academic researchers and comes as part of the phrap package, but you must obtain a license to get the software. Further information on how to obtain phrap/cross_match/swat is available on the official website for phred, phrap and consed.